From out of the Ashes
by Merwholocked628
Summary: It's his fault, he doesn't know why or how but it's his fault. It's his fault Earth is destroyed, it's his fault a bunch of kids have to pick up the pieces. Because, maybe, just maybe, he was the world's destroyer. Good!Doctor vs. Dark!Doctor
1. Chapter 1

**I felt the need to live up to my name and write a Doctor Who fan fiction, Mostly 'OC's' but The Doctor and a few companions are thrown in there. Please review I love to hear from you. I don't own Doctor Who. Chapter 1 onwards!**

The Doctor was quite used to staring down a barrel of a gun. Not to say he particularly liked it of course but it was one of the many reactions he had faced when he hopped out of his magic blue box. But he didn't expect the owner of the gun to be a child, nor for that child to know his name.

"How dare you?!" The boy growled, his icy blue eyes boring into the Doctors. "How dare you wear the clothes you once wore? How dare you dress like the Doctor?" His gold-rimmed glasses glinted in the light of the setting sun.

The Time-lord flailed around a bit before settling into one of his famous rambles;

"Um well, you see, I am the Doctor, uh, how do you know my name? Where am I? Looks like Earth, but can't be, nowhere are all the humans? So, what planet is this, and who are you?" 

The boy huffed impatiently "Time traveler, should've known." His eyes narrowed a bit behind his glasses "If you must know yes, this is Earth. And all the people, they are in enslavement camps just as you ordered. I'm Commander Daniel Williams, and don't expect me to bow to you _sir._" The boy-Daniel spat the last word as if it were poison.

The Doctor gasped. "M-me? I would never...This...This wasn't ME!"

"Look around you, this is all you_._ All of it!"

And so the Time-lord for once in his life did as he was told. The air was thick and humid, crumbling buildings stood all around them. The sky, for the most part, was black with swirling clouds blotting out all but a single ray of sun that glinted off the Commanders frames. The Doctor took a closer look at the boy himself, and his heart dropped. Daniel was older than he had first thought him to be, maybe around fourteen, but he wasn't nearly old enough for the look in his eye, it was the look the Doctor saw himself when he glanced in a mirror. One of someone who had had everyone they cared for ripped away from them. He wore a military uniform, a black heavy coat with a black t-shirt underneath. Dark (black) Cargo pants and knee-high combat boots well worn with brass buckles. His gun was an oddity, now that it was, thankfully, not pointed at him, The Doctor could see it was covered with wires and such. And most hauntingly of all, when the boy shifted, he could see a scar wrapped around his wrist, like handcuffs that had been pulled too tight.

"Had enough?" Commander Williams pulled out a length of rope. "We don't have handcuffs so this'll have to do. I have orders to bring you in. Well, not you, you I guess but still."

"Right, Okay then." The Doctor gulped, trying to sound brave. "Geronimo!" He said in a voice that was barely a whisper.

Daniel smirked a bit, probably laughing at his own private joke, before ushering him away.

The building he was led to had probably been a school in another life.

"We call it the Neberkenezer. Our own little sick joke I guess." Daniel shrugged.

It was all the Doctor could do to nod. "Who are you then, Morpheus?" he laughed weakly. 

"No, that would probably be Director Hahn."

The Time-lord tried, with as much dignity as he could manage, to straighten his bow tie with his chin as the Commander slid a card through a slot and the door unlocked.

The inside confirmed it; it had most definitely been a school once upon a time. But the insides were scorched in places and the grey tile was cracking. Daniel took off his beanie (also black) to reveal a mop of brown hair that probably hadn't been washed in a long time. The boy maneuvered him to place that had probably once been the counselor's office judging by the sign that said

_c u l rs 100_

"In here." The Doctor was pushed into the room, which normally he would be cross about but he had the sinking suspicion that everyone hated him and he would like to find out why.

Inside a boy with a very serious expression was currently spinning in an office chair. He was a lot taller than Daniel but about the same age. Once he got a glance at the Commander and The Doctor he stopped and turned his blue/grey gaze on them

"Commander?" He gestured to the Doctor as if to say _Explain._

Daniel saluted. "His ship just appeared sir! I did as you commanded and brought him in. He claims to have no idea what is going on here."

The boy looked The Doctor over once. "Call in Em. She's our resident Whovian. I'm sure she can set the story straight." And for the first time the boy cracked a smile.

Daniel pretended to look hurt. "Hey, if she's our 'Resident Whovian' what am I Dillon? Chopped liver?" 

"Yes." Dillon nodded once for emphasis. "Just call her in."

"Hello, sorry Doctor lost, Doctor very confused. Who are you, what's a Whovian, what's the square root of Jelly babies, wait what was I saying?" The Timelord would've held out a hand had they not been tied behind his back.

"Director Dillon Hahn." Dillon answered formally trying extremely hard not to laugh. "And a Whovian? Well I better let Em explain."

"And, I'm under the impression that everyone hates me, mind telling me why?"

Dillon sighed, suddenly looking like an old man. "Now that is very, very hard to explain."

Fortunately he didn't need to, for just then a girl came rushing in. She had very short light brown hair with bangs that fell over one eye. Her uniform was an exact replica of Daniel and Dillon's but she wore a scorched lab coat over hers.

"Em! That was quick." Dillon said tearing his gaze away from the Doctor.

"You called me?" She looked genuinely confused.

"Isn't that why you're here?"

She shook her head quickly. "We, uh have a problem."

Dillon and Daniel ran to the doorway immediately. Well, Dillon did. Daniel first had to grab the now EXTREMELY confused Doctor.

They all charged down a hallway to a large room filled with computers. A large cursive B was on each one, and a garbled voice was repeating;

_We know where you are rejects. You're dead._

"It's Bennett." Em repeated solemnly. And Dillon sucked in a breath.

"Hi, Doctor again!" The Time Lord interrupted. "Doctor stiilllll confused."

Em jumped about three feet in the air and spun around looking a mixture of horrified and excited.

When she saw who spoke she tried her best to look angry but it just looked like she wanted to hug him.

"Why is he here?" She tried to spit out the words but it sounded like an excited squeal.

Before anyone could the Doctor jumped in. "I was just traveling but then this lot" He pointed behind him, "pointed a gun at me, care to explain why? And while you're at it, who's Bennett? And rejects?"

Em shifted uncomfortably. "Well Bennett, we are not completely sure, but we think he/she might have been a friend of ours in Old World Bethany she was called back then." Dillon visibly sighed and the girl continued, "But we know he or she is a hacker, with incredible skills. As for rejects, that's us. We were Lab rats for the...well you. But we escaped, and somehow the testing did something to us." She knocked on her skull. "We're faster, smarter, stronger than we ever were back in old world, but escapees are called rejects."

"FOR THE LOVE OF GALLIFREY WOULD SOMEONE TELL ME WHAT THE HELL I DID?" The Doctor yelled, causing everyone to jump.

Em opened her mouth to speak but then the computers blared and a figure appeared on screen.

**Good? Not good? Please give me any constructive criticism you have.**


	2. Chapter 2

**HI BETHANY! You're my only follower at the moment so I'm just going to talk to you;**

**So how you been?**

**Good.**

**So how are your fandoms today?**

**That's good.**

**When I say Discord please don't think MLP I couldn't figure out what to call him. Okay let's just get on with the story. I do not own Doctor Who. (If I did so many headcanons. So many.)**

Bennett scratched at her arm where the electro-cables had been implanted. The irritation was a small price to play for her new life. She had been reborn and as payment all she had to do was follow simple commands. And why wouldn't she? She loved Discord, worshipped him, of course she would do his bidding.

Her fingers flew across the keyboard. The rejects system was a challenge to hack into but nothing could keep her out. And soon the firewall cleared and Bennett was free to install the video, as well as see any important messages they had received from that bloody Captain Jack Harkness.

"It's up." Her voice was hoarse and dry as if she hadn't used it in awhile. Which she hadn't, she didn't need to speak to do Discord's bidding.

"Good." A voice purred from the darkness. "Turn on the camera." Which Bennett did falling back into silence.

The alarms attracted the few kids still roaming the halls. A tall boy who was as thin as paper, a slightly shorter boy with what looked like the remnants of a skater haircut and an asian girl with a trench coat and a disapproving look. Em glanced at the girl and motioned her closer.

The Doctor peered at the screen, pulling out his old glasses for a closer look. The figure on the screen grew clearer and The Doctor could see that it. Was. Him.

But not him. The man was wearing a black tweed coat and a grey bow tie. His blue eyes twinkled but not with childlike giddiness like The Doctor's. With malice like every villain he'd ever faced.

The man on screen began to speak, his voice the exact same as the Doctor's but with a dark undertone to it.

"Huh. I forgot about this day." The man smirked at The Doctor. "I guess this is when it all started, or when it all ended. Depending on your point of view." he shrugged, giving The Doctor a meaningful smile.

And that's when the Time-lord lost it. "Look." he growled, his voice taking on an unusual note of anger. "I just landed here. I have no idea what's going on, and if you're me you know I hate not knowing things. And now you're telling me that I, one day will create all this! No. Ever hear that word? It means NO."

The man just smirked and shook his head before motioning towards the side of the screen.

A girl about the age of the children around him stepped in to The Doctor's line of view. She had strawberry blonde hair and very pale skin. All except for a line of red, circles and lines leading from her right hand to her cheek.

Dillon sucked in a breath. Em and the asian girl looked over sympathetically,

'I'm sorry.' They both mouthed, and Em bit her lip looking back at the girl on the screen. The asian girl put her disapproving look back on. But this time, thankfully, it was not directed at him.

The girl grinned at the dark man and then looked right at the band of rejects. Her pale blue eyes made her look like she was blind. Or possessed. She only said one word, in a raspy voice,

"Ex-ter-min-ate." And pointed a finger gun at them. The screen clicked off and went black.

"A.G!" Director Hahn called, motioning to the asian girl. "Get Torchwood on the phone! And don't let Discord know you're doing it."

The girl nodded "Yes sir." And gave him a two finger salute.

"A.G! Wait!" Em ran up to the girl. "Use this." She dug in the pocket of her scorched lab coat and pulled out an old cell phone with a bunch of old wires and gizmo's sticking out of it. "Use this. It'll only work for a few minutes so no awkwardness I know how you are on phones." Em gave A.G a look and they both had to stifle giggles.

"Anyway." Em continued. "It's unhackable I had Devin try it and you know he's almost as good as Beth-I mean Bennett."

A.G nodded and took the phone.

"Daniel!" Dillon continued. "Take Trystn," He pointed to the skinny kid. "And Hunter." The skater haired kid. "And guard the front entrance. I'll take Devin and guard the back." With that they turned on their heels and left.

"Oh and Em?" Director Hahn called from over his shoulder. "Make sure those new prototypes work. And brief the Doctor. Quickly."

The short haired girl nodded and took The Doctor by the hand. "Here let me show you."

"About time." The alien muttered.

Em lead him up a cracked flight of stairs into a huge room.

"It used to be our library." Em explained opening the door to let him pass. "Now it's my laboratory."

"But why." The Doctor said. "What happened? Why isn't it still a library?" He was desperate to know now.

Em sighed. "We don't have much time so I'll give you the short version. Basically, we woke up one morning and every screen had Discord's face on it, that's what we call the dark version of you, the sky was filled with Daleks, and, and our parents were either killed or enslaved. Only those who were clever enough were nominated for "Rehabilitation. That's what Bennett went through. It didn't work on us though, we escaped before it could. That's why we're called rejects." As promised she said this all very fast.

"So the Daleks destroyed everything? Why wasn't Discord killed?"

"Somehow he can control them. I'm still trying to figure out how."

"One more question." The Doctor grinned at the child.

"Okay, One." She gave a small nervous smile.

"How many people are left at Torchwood?"

Em thought for a moment "Well Jack obviously, and his boyfriend Ianto, a girl named Tosh and a man named Owen. Only Gwen Cooper died."

The Doctor bowed his head and Em fiddled with some more of the odd guns on a small table.

They sat in silence for a few moments when all the sudden a robotic like call screamed.

"EX-TER-MIN-ATE!" Glass shattered downstairs.

Em glanced up a little panicked. "Bennett's slower this time." Then she scooped up the guns, threw one at the Doctor despite his protests and tore out of the room.


	3. Chapter 3

**- Chapter 3**

The dull blare of the alarms echoed throughout the corridors and soon were followed by screams.

"EMILY!" Commander Williams shouted over the cries of the Daleks and the blare of the alarms, to the girl racing down the stairs.

Em jumped the railing "Here!" She tossed the gun to him. "New and impro-AHHHHHHH!" She screamed as a Dalek shot at her.

The Doctor buzzed his sonic screwdriver, trying to jam the Daleks whisk-gun-thing. "Got it! We've only got a few minutes so…."

"JUST SHOOT THE DARN THING!" Daniel and Em yelled, pulling out their guns.

"Guns and me don't get along!" The Doctor crossed his arms and pouted like a sulky child.

Daniel rolled his eyes and clicked the trigger of his own gun before staring at Emily in horror.

"They don't work." He said his voice dangerously calm

Em looked terrified. She jumped out of the way of a few Dalek death whisks before squeaking;

"But I checked them myself! I blew up the bleachers for god sake!"

Daniel sighed as if this was just a minor annoyance and roundhouse kicked the closest Dalek.

The Doctor nodded his approval and joined the fight, sonicking the nearest Dalek effectively confusing it and making the creature spin in circles.

Meanwhile A.G was currently hiding in what looked to be a large Janitors closet.

"Just get him here!" She snapped impatiently in the odd looking cellphone she had been holding.

The person on the other line said something that caused A.G to growl in frustration.

"Ianto, I don't care if he's dead at the moment! GET JACK HERE NOW!" The girl just finished her sentence when the line went dead.

"Great. Just great." She muttered before smashing the now useless device on the floor.

"I. Hate. The. Fricken. World." She screamed stomping on the phone to emphasis every word.

The Daleks must of heard her because the door was blown off its hinges and landed on A.G knocking her to the ground.

"FIND THE FEMALE!" The three aliens screamed pointing their..erm...whisks around the room.

A.G pulled herself up, felt around on the floor for her glasses, roughly shoved them on her face before gasping.

"You. Broke. My. Glasses." She whispered her voice shaking with rage. The shatter pattern did look interesting from the inside she mused before the Daleks broke her concentration with their usual cry of 'Exterminate'

"You know what? That's getting kinda boring, why don't you try something new?" A.G cocked her head as if she was considering the Daleks, "Like dying in a hole." To emphasise her point she roundhouse kicked the nearest Dalek sending it flying down the hallway.

"EXTERMINATE!"

"I GET IT! You want me to 'Ex-ter-min-ate you. Don't know why you're suicidal but, hey I'm not complaining." She shrugged before kicking another of the creatures.

"Anyone else?" A.G asked before jumping up on a table and hoisting herself into an air vent, the last Dalek trying in vain to shoot at her.

Em had apparently had had enough of trying to punch and kick the Daleks. She pulled out two wicked looking daggers from her boots and clicked a button on the hilts, the tip grew red hot and blue liquid seeped through microscopic holes in the blade, once it had effectively coated all of the blade Em threw both of the daggers, they pierced through two of the Daleks armor and the aliens stopped in their tracks.

"What...the ….heck was that?" Daniel panted, happy when the Doctor pulled out his sonic and jammed the four aliens he had been fighting's guns.

Em pulled out the daggers and slid them back in her boots. "Tosh gave them to me, Alien tech, can't figure out how it works or how to replicate it." She frowned thoughtfully. "The poison is usually deadly, but I only managed to paralyze them. Sorry."

Commander Williams nodded a bit pale. "Oh well….it's nice to know you could murder everyone if you wanted to."

"Oh not everyone. Maybe four or five people, but thats the limit before I'd have to refill the poison, I have a charging agent in my boots." Em smiled weakly, her face now betraying how tired she really was.

"Director Hahn." Williams said into the small communicator that was strapped to his coat.

"Not….a….good…..time….." Came the slightly garbled reply.

"All our Daleks are incapacitated and I'm sending Em and the Doctor to FIX the guns." He gave the short haired girl a meaningful look. "So I'll come help."

"Copy."

"Okay Em, you heard me." Daniel said pushing up his now bent spectacles. "Go fix them….oh and find A.G while you're at it."

"Yes Sir! This way!" Em shouted tugging the Doctor towards one of her 'old' labratory's. Really they weren't that old, the school was rather new but Em was in charge of designing and making the weapons for the rejects, and sometimes it, well, exploded.

"EX-TER-MIN-ATE!"

"Not that way! Do not go that way!" The duo screamed as they raced back the way they came.

"I lied, this way!" Em shouted again thanking every god she could name that she had four or five labs scattered around the building.

After a lot of screaming and flailing they finally made it too one of the labs where Em had started randomly connecting wires to bits and bobs in a pattern that only made sense to her.

Meanwhile Dillon, Trystn, Hunter, and Daniel were fighting a losing battle. No matter what they did the Daleks didn't stop there advances. Trystn took out his Katana (no one wanted to know where he had been hiding it) and started slashing off the Daleks eye stocks which seemed to work for a time before the aliens got smart and did some quick 'upgrades' to their armor.

Hunter tried in vain to shoot at the Daleks with his normal bullets but even a machine gun didn't do anything to help. Dillon to a spiked baseball bat to the things but barely put a dent in their armor.

Suddenly there was a little 'pop' and a blast from behind the Daleks, the metal monstrosities all burst into flame. And there was the team of Torchwood looking heroic behind the blaze.

"Did someone order a ridiculously handsome hero?" Jack questioned.


End file.
